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Rhizobia are diazotrophic
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
that fix nitrogen after becoming established inside the root nodules of
legume A legume () is a plant in the family Fabaceae (or Leguminosae), or the fruit or seed of such a plant. When used as a dry grain, the seed is also called a pulse. Legumes are grown agriculturally, primarily for human consumption, for livestock for ...
s (
Fabaceae The Fabaceae or Leguminosae,International Code of Nomenc ...
). To express genes for
nitrogen fixation Nitrogen fixation is a chemical process by which molecular nitrogen (), with a strong triple covalent bond, in the air is converted into ammonia () or related nitrogenous compounds, typically in soil or aquatic systems but also in industry. Atmo ...
, rhizobia require a
plant Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae excl ...
host; they cannot independently fix
nitrogen Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...
. In general, they are gram negative, motile, non- sporulating rods. Rhizobia are a "group of soil bacteria that infect the roots of legumes to form
root nodules Root nodules are found on the roots of plants, primarily legumes, that form a symbiosis with nitrogen-fixing bacteria. Under nitrogen-limiting conditions, capable plants form a symbiotic relationship with a host-specific strain of bacteria kno ...
". Rhizobia are found in the soil and after infection, produce nodules in the
legume A legume () is a plant in the family Fabaceae (or Leguminosae), or the fruit or seed of such a plant. When used as a dry grain, the seed is also called a pulse. Legumes are grown agriculturally, primarily for human consumption, for livestock for ...
where they fix nitrogen gas (N2) from the atmosphere turning it into a more readily useful form of nitrogen. From here, the nitrogen is exported from the nodules and used for growth in the legume. Once the legume dies, the nodule breaks down and releases the rhizobia back into the soil where they can live individually or reinfect a new legume host.


History

The first known
species In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriat ...
of rhizobia, '' Rhizobium leguminosarum'', was identified in 1889, and all further species were initially placed in the ''
Rhizobium ''Rhizobium'' is a genus of Gram-negative soil bacteria that fix nitrogen. ''Rhizobium'' species form an endosymbiotic nitrogen-fixing association with roots of (primarily) legumes and other flowering plants. The bacteria colonize plant cells ...
''
genus Genus ( plural genera ) is a taxonomic rank used in the biological classification of living and fossil organisms as well as viruses. In the hierarchy of biological classification, genus comes above species and below family. In binomial nom ...
. Most research has been done on
crop A crop is a plant that can be grown and harvested extensively for profit or subsistence. When the plants of the same kind are cultivated at one place on a large scale, it is called a crop. Most crops are cultivated in agriculture or hydropon ...
and
forage Forage is a plant material (mainly plant leaves and stems) eaten by grazing livestock. Historically, the term ''forage'' has meant only plants eaten by the animals directly as pasture, crop residue, or immature cereal crops, but it is also use ...
legumes such as
clover Clover or trefoil are common names for plants of the genus ''Trifolium'' (from Latin ''tres'' 'three' + ''folium'' 'leaf'), consisting of about 300 species of flowering plants in the legume or pea family Fabaceae originating in Europe. The genus ...
,
alfalfa Alfalfa () (''Medicago sativa''), also called lucerne, is a perennial flowering plant in the legume family Fabaceae. It is cultivated as an important forage crop in many countries around the world. It is used for grazing, hay, and silage, as ...
,
bean A bean is the seed of several plants in the family Fabaceae, which are used as vegetables for human or animal food. They can be cooked in many different ways, including boiling, frying, and baking, and are used in many traditional dishes th ...
s,
pea The pea is most commonly the small spherical seed or the seed-pod of the flowering plant species ''Pisum sativum''. Each pod contains several peas, which can be green or yellow. Botanically, pea pods are fruit, since they contain seeds and d ...
s, and
soybean The soybean, soy bean, or soya bean (''Glycine max'') is a species of legume native to East Asia, widely grown for its edible bean, which has numerous uses. Traditional unfermented food uses of soybeans include soy milk, from which tofu ...
s; more research is being done on North American legumes.


Taxonomy

Rhizobia are a
paraphyletic In taxonomy, a group is paraphyletic if it consists of the group's last common ancestor and most of its descendants, excluding a few monophyletic subgroups. The group is said to be paraphyletic ''with respect to'' the excluded subgroups. In ...
group that fall into two classes of
Pseudomonadota Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria. The renaming of phyla in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature. Th ...
—the alphaproteobacteria and betaproteobacteria. As shown below, most belong to the order Hyphomicrobiales, but several rhizobia occur in distinct bacterial orders of the Pseudomonadota. These groups include a variety of non-
symbiotic Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or para ...
bacteria. For instance, the plant
pathogen In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a g ...
''
Agrobacterium ''Agrobacterium'' is a genus of Gram-negative bacteria established by H. J. Conn that uses horizontal gene transfer to cause tumors in plants. ''Agrobacterium tumefaciens'' is the most commonly studied species in this genus. ''Agrobacterium ...
'' is a closer relative of ''Rhizobium'' than the ''Bradyrhizobium'' that nodulate soybean.


Importance in agriculture

Although much of the nitrogen is removed when
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
-rich
grain A grain is a small, hard, dry fruit ( caryopsis) – with or without an attached hull layer – harvested for human or animal consumption. A grain crop is a grain-producing plant. The two main types of commercial grain crops are cereals and legum ...
or hay is
harvest Harvesting is the process of gathering a ripe crop from the fields. Reaping is the cutting of grain or pulse for harvest, typically using a scythe, sickle, or reaper. On smaller farms with minimal mechanization, harvesting is the most l ...
ed, significant amounts can remain in the soil for future crops. This is especially important when nitrogen
fertilizer A fertilizer (American English) or fertiliser (British English; see spelling differences) is any material of natural or synthetic origin that is applied to soil or to plant tissues to supply plant nutrients. Fertilizers may be distinct from ...
is not used, as in
organic Organic may refer to: * Organic, of or relating to an organism, a living entity * Organic, of or relating to an anatomical organ Chemistry * Organic matter, matter that has come from a once-living organism, is capable of decay or is the product ...
rotation schemes or some less-
industrialized Industrialisation ( alternatively spelled industrialization) is the period of social and economic change that transforms a human group from an agrarian society into an industrial society. This involves an extensive re-organisation of an econ ...
countries.
Nitrogen Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...
is the most commonly deficient nutrient in many soils around the world and it is the most commonly supplied plant nutrient. Supply of nitrogen through fertilizers has severe environmental concerns. Specific strains of rhizobia are required to make functional nodules on the roots able to fix the N2. Having this specific rhizobia present is beneficial to the legume, as the N2 fixation can increase crop yield. Inoculation with rhizobia tends to increase yield. Legume inoculation has been an agriculture practice for many years and has continuously improved over time. 12–20 million hectares of soybeans are inoculated annually. The technology to produce these inoculants are microbial fermenters. An ideal inoculant includes some of the following aspects; maximum efficacy, ease of use, compatibility, high rhizobial concentration, long shelf-life, usefulness under varying field conditions, and survivability. These inoculants may foster success in legume cultivation. As a result of the nodulation process, after the harvest of the crop there are higher levels of soil nitrate, which can then be used by the next crop.


Symbiotic relationship

Rhizobia are unique in that they are the only nitrogen-fixing bacteria living in a
symbiotic Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or para ...
relationship with
legumes A legume () is a plant in the family Fabaceae (or Leguminosae), or the fruit or seed of such a plant. When used as a dry grain, the seed is also called a pulse. Legumes are grown agriculturally, primarily for human consumption, for livestock for ...
. Common crop and forage legumes are peas, beans, clover, and soy.


Nature of the mutualism

The legume–rhizobium
symbiosis Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or para ...
is a classic example of mutualism—rhizobia supply ammonia or
amino acids Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
to the plant and in return receive organic acids (principally as the
dicarboxylic acid In organic chemistry, a dicarboxylic acid is an organic compound containing two carboxyl groups (). The general molecular formula for dicarboxylic acids can be written as , where R can be aliphatic or aromatic. In general, dicarboxylic acids sho ...
s malate and succinate) as a carbon and energy source. However, because several unrelated strains infect each individual plant, a classic tragedy of the commons scenario presents itself. Cheater strains may hoard plant resources such as
polyhydroxybutyrate Polyhydroxybutyrate (PHB) is a polyhydroxyalkanoate (PHA), a polymer belonging to the polyesters class that are of interest as bio-derived and biodegradable plastics. The poly-3-hydroxybutyrate (P3HB) form of PHB is probably the most common type ...
for the benefit of their own
reproduction Reproduction (or procreation or breeding) is the biological process by which new individual organisms – "offspring" – are produced from their "parent" or parents. Reproduction is a fundamental feature of all known life; each individual or ...
without fixing an appreciable amount of
nitrogen Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...
. Given the costs involved in nodulation and the opportunity for rhizobia to cheat, it may be surprising that this symbiosis should exist at all.


Infection and signal exchange

The formation of the symbiotic relationship involves a signal exchange between both partners that leads to mutual recognition and development of symbiotic structures. The most well understood mechanism for the establishment of this symbiosis is through intracellular infection. Rhizobia are free living in the soil until they are able to sense
flavonoid Flavonoids (or bioflavonoids; from the Latin word ''flavus'', meaning yellow, their color in nature) are a class of polyphenolic secondary metabolites found in plants, and thus commonly consumed in the diets of humans. Chemically, flavonoids ...
s, derivatives of 2-phenyl-1.4-benzopyrone, which are secreted by the roots of their host plant triggering the accumulation of a large population of cells and eventually attachment to root hairs. These flavonoids then promote the DNA binding activity of NodD which belongs to the LysR family of transcriptional regulators and triggers the secretion of nod factors after the bacteria have entered the root hair. Nod factors trigger a series of complex developmental changes inside the root hair, beginning with root hair curling and followed by the formation of the infection thread, a cellulose lined tube that the bacteria use to travel down through the root hair into the root cells. The bacteria then infect several other adjacent root cells. This is followed by continuous cell proliferation resulting in the formation of the root nodule. A second mechanism, used especially by rhizobia which infect aquatic hosts, is called crack entry. In this case, no root hair deformation is observed. Instead the bacteria penetrate between cells, through cracks produced by lateral root emergence. Inside the nodule, the bacteria differentiate morphologically into bacteroids and fix atmospheric nitrogen into
ammonium The ammonium cation is a positively-charged polyatomic ion with the chemical formula or . It is formed by the protonation of ammonia (). Ammonium is also a general name for positively charged or protonated substituted amines and quaterna ...
, using the enzyme nitrogenase.
Ammonium The ammonium cation is a positively-charged polyatomic ion with the chemical formula or . It is formed by the protonation of ammonia (). Ammonium is also a general name for positively charged or protonated substituted amines and quaterna ...
is then converted into amino acids like glutamine and
asparagine Asparagine (symbol Asn or N) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH form under biological conditions), an α-carboxylic acid group (which is in the depro ...
before it is exported to the plant. In return, the plant supplies the bacteria with
carbohydrate In organic chemistry, a carbohydrate () is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula (where ''m'' may o ...
s in the form of organic acids. The plant also provides the bacteroid oxygen for
cellular respiration Cellular respiration is the process by which biological fuels are oxidised in the presence of an inorganic electron acceptor such as oxygen to produce large amounts of energy, to drive the bulk production of ATP. Cellular respiration may be des ...
, tightly bound by leghaemoglobins, plant proteins similar to human
hemoglobin Hemoglobin (haemoglobin BrE) (from the Greek word αἷμα, ''haîma'' 'blood' + Latin ''globus'' 'ball, sphere' + ''-in'') (), abbreviated Hb or Hgb, is the iron-containing oxygen-transport metalloprotein present in red blood cells (erythroc ...
s. This process keeps the nodule oxygen poor in order to prevent the inhibition of nitrogenase activity. Recently, a ''
Bradyrhizobium ''Bradyrhizobium'' is a genus of Gram-negative soil bacteria, many of which fix nitrogen. Nitrogen fixation is an important part of the nitrogen cycle. Plants cannot use atmospheric nitrogen (N2); they must use nitrogen compounds such as nitrate ...
'' strain was discovered to form nodules in ''
Aeschynomene ''Aeschynomene'' is a genus of flowering plants in the family Fabaceae, and was recently assigned to the informal monophyletic ''Dalbergia'' clade of the Dalbergieae. They are known commonly as jointvetches. These legumes are most common in warm ...
'' without producing nod factors, suggesting the existence of alternative communication signals other than nod factors, possibly involving the secretion of the plant hormone cytokinin. It has been observed that root nodules can be formed spontaneously in ''
Medicago ''Medicago'' is a genus of flowering plants, commonly known as medick or burclover, in the legume family (Fabaceae). It contains at least 87 species and is distributed mainly around the Mediterranean basin. The best-known member of the genus is ...
'' without the presence of rhizobia. This implies that the development of the nodule is controlled entirely by the plant and simply triggered by the secretion of nod factors.


Evolutionary hypotheses


The sanctions hypothesis

There are two main hypotheses for the mechanism that maintains legume-rhizobium symbiosis (though both may occur in nature). The sanctions hypothesis theorizes that legumes cannot recognize the more parasitic or less nitrogen fixing rhizobia, and must counter the parasitism by post-infection legume sanctions. In response to underperforming rhizobia, legume hosts can respond by imposing sanctions of varying severity to their nodules. These sanctions include, but are not limited to reduction of nodule growth, early nodule death, decreased carbon supply to nodules, or reduced
oxygen Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements ...
supply to nodules that fix less nitrogen. Within a nodule, some of the bacteria differentiate into nitrogen fixing bacteroids, which have been found to be unable to reproduce. Therefore, with the development of a symbiotic relationship, if the host sanctions hypothesis is correct, the host sanctions must act toward whole nodules rather than individual bacteria because individual targeting sanctions would prevent any reproducing rhizobia from proliferating over time. This ability to reinforce a mutual relationship with host sanctions pushes the relationship toward a mutualism rather than a parasitism and is likely a contributing factor to why the symbiosis exists. However, other studies have found no evidence of plant sanctions.


The partner choice hypothesis

The partner choice hypothesis proposes that the plant uses prenodulation signals from the rhizobia to decide whether to allow nodulation, and chooses only noncheating rhizobia. There is evidence for sanctions in soybean plants, which reduce rhizobium reproduction (perhaps by limiting oxygen supply) in nodules that fix less nitrogen. Likewise, wild lupine plants allocate fewer resources to nodules containing less-beneficial rhizobia, limiting rhizobial reproduction inside. This is consistent with the definition of sanctions, although called "partner choice" by the authors. Some studies support the partner choice hypothesis. While both mechanisms no doubt contribute significantly to maintaining rhizobial cooperation, they do not in themselves fully explain the persistence of the mutualism. The partner choice hypothesis is not exclusive from the host sanctions hypothesis, as it is apparent that both of them are prevalent in the symbiotic relationship.


Evolutionary history

The symbiosis between nitrogen fixing rhizobia and the legume family has emerged and evolved over the past 66 million years. Although evolution tends to swing toward one species taking advantage of another in the form of noncooperation in the selfish-gene model, management of such symbiosis allows for the continuation of cooperation. When the relative fitness of both species is increased, natural selection will favor the symbiosis. To understand the evolutionary history of this symbiosis, it is helpful to compare the rhizobia-legume symbiosis to a more ancient symbiotic relationship, such as that between endomycorrhizae fungi and land plants, which dates back to almost 460 million years ago. Endomycorrhizal symbiosis can provide many insights into rhizobia symbiosis because recent genetic studies have suggested that rhizobia co-opted the signaling pathways from the more ancient endomycorrhizal symbiosis. Bacteria secrete Nod factors and endomycorrhizae secrete Myc-LCOs. Upon recognition of the Nod factor/Myc-LCO, the plant proceeds to induce a variety of intracellular responses to prepare for the symbiosis. It is likely that rhizobia co-opted the features already in place for endomycorrhizal symbiosis, because there are many shared or similar genes involved in the two processes. For example, the plant recognition gene, SYMRK (symbiosis receptor-like kinase) is involved in the perception of both the rhizobial Nod factors as well as the endomycorrhizal Myc-LCOs. The shared similar processes would have greatly facilitated the evolution of rhizobial symbiosis, because not all the symbiotic mechanisms would have needed to develop. Instead the rhizobia simply needed to evolve mechanisms to take advantage of the symbiotic signaling processes already in place from endomycorrhizal symbiosis.


Other diazotrophs

Many other species of bacteria are able to fix nitrogen (
diazotroph Diazotrophs are bacteria and archaea that fix gaseous nitrogen in the atmosphere into a more usable form such as ammonia. A diazotroph is a microorganism that is able to grow without external sources of fixed nitrogen. Examples of organisms tha ...
s), but few are able to associate intimately with plants and colonize specific structures like legume nodules. Bacteria that do associate with plants include the
actinomycete The Actinomycetales is an order of Actinomycetota. A member of the order is often called an actinomycete. Actinomycetales are generally gram-positive and anaerobic and have mycelia in a filamentous and branching growth pattern. Some actinomycete ...
, '' Frankia'', which form symbiotic root nodules in
actinorhizal plant Actinorhizal plants are a group of angiosperms characterized by their ability to form a symbiosis with the nitrogen fixing actinomycetota ''Frankia''. This association leads to the formation of nitrogen-fixing root nodules. Classification Actinor ...
s, although these bacteria have a much broader host range implying the association is less specific than in legumes. Additionally, several
cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
like ''
Nostoc ''Nostoc'', also known as star jelly, troll’s butter, spit of moon, fallen star, witch's butter (not to be confused with the fungi commonly known as witches' butter), and witch’s jelly, is the most common genus of cyanobacteria found in var ...
'' are associated with aquatic ferns, '' Cycas'' and '' Gunneras,'' although they do not form nodules. Additionally, loosely associated plant bacteria, termed endophytes, have been reported to fix nitrogen ''in planta''. These bacteria colonize the intercellular spaces of leaves, stems and roots in plants but do not form specialized structures like rhizobia and '' Frankia.'' Diazotrophic bacterial endophytes have very broad host ranges, in some cases colonizing both monocots and dicots.


References


Further reading

* {{Cite journal , last1=Jones , first1= KM , title=How rhizobial symbionts invade plants: the Sinorhizobium–Medicago model , journal=Nature Reviews Microbiology , volume=5 , issue=8 , pages=619–33 , year=2007 , pmid=17632573 , doi=10.1038/nrmicro1705 , last2=Kobayashi , first2=H , last3=Davies , first3=BW , last4=Taga , first4=ME , last5=Walker , first5=GC , pmc=2766523 , display-authors=etal


External links


Legume sanctions maintain Rhizobium mutualism

Current list of rhizobia species

Nitrogen Fixation and Inoculation of Forage Legumes
Hyphomicrobiales Symbiosis Nitrogen cycle Soil biology